Permit me to be coarse for the sake of simplicity and tell you that the only LaTeX template you should spend your time and energy on is tufte-latex: http://news.ycombinator.com/item?id=1572530.
It even has a snazzy guide for setting it up on Stack Exchange: http://tex.stackexchange.com/questions/6483/setting-up-a-lat....
It’s pretty much all you need, and configuring LaTeX can turn into a rabbit hole you will never get out of. Try writing your project in tufte-latex, and I am sure you’ll find that it fits the bill perfectly. I do recall something about having to install an additional package to colour the hyperlinks or something to that extent, though.
I have some old templates—even some boilerplate lying around—so you can drop me a tweet or something, if it isn’t working for you, and I’ll throw something up in a gist.